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Introduction

"...Utopia Documents v2.4 is a free PDF reader that connects the static content of scientific articles to the dynamic world of online content. With a brand new look and feel that blend real-time updates with the typographic elegance of published articles, Utopia Documents brings up-to-date information directly to your desktop..."

"...scientific research is no walk in the park, but anyone who’s ever worked in it will agree that finding, reading, and citing articles is one of the most time-consuming tasks. Utopia Documents is a free research utility aimed at making this task easier by offering a PDF reader with built-in exploration tools and other research aids. Although it can be considered as a direct competitor to services like Mendeley, Zotero and ReadCube, Utopia Documents is actually different from all three, and even sports a Mendeley integration..."— New Technology, 2013

Utopia Documents - http://utopiadocs.com is a "smart, scientific, semantic" free PDF reader that connects static "print" text of scientific articles to dynamic online web content. Consequently, Utopia Documents ‘brings to life’ e-versions of scientific papers by adding interactive (and social) elements. The software offers readers access to original research and analytical tools to explore research findings in real time. By providing access to metadata, Utopia allows users to browse relationships articles have with other scientific content. The intelligent semantic reader of Utopia Documents is used to publish the Biochemical Journal - and enriches the experience of reading PDFs on-line. Utopia does this by generating formatted citations with bibliographic links to cited articles, and provides access to document metadata. Readers can also highlight and explore a vast semantic ‘linked data’ space by finding terms they themselves want to define. Various extensions provide links to blogs, open data and social media to find related information. The reader bridges 'linkability gaps' between HTML and PDF, making the latter as linked-in to web discussions as the former. Further, it allows readers to experience dynamically-enriched scientific content.

Background

In 2012, in collaboration with AQnowledge - semantics for science, Lost Island Labs released version 2.0 of Utopia Documents. It is freely available from http://utopiadocs.com/, and currently available for Mac, Windows and Linux. Its purpose is to help science move forward collaboratively. Because scientific knowledge is often ‘buried’ in static content, fragments of knowledge are buried in the web. Countless hours of time are wasted by repeating scientific experiments or by trying to verify facts known to be false. Utopia enables scientists to get the most from the literature by joining these disparate elements.

Software features

You can use Utopia Documents in the same way as any other PDF reader, such as Adobe Acrobat Reader or the Preview application on a Mac. The application's workspace is split into three main panes: the PDF file itself is displayed on the left, a 'pager' is displayed at the bottom, and a light-blue sidebar to the right. The pager allows you to scan back and forth through the document and to move rapidly from one page to another. Although you can use Utopia Documents to look at any PDF file, the software really comes into its own as a reader for scholarly papers in the biomedical and biochemical fields.

Free PDF reader available for Windows, Mac and Linux

Recognizes documents by creating unique ‘fingerprints’ of contents as they are rendered

Fingerprints are created on the basis of interalia or key typographical and bibliometric characteristics (authors, figures, references etc.)

PDFs are "transformed from a digital facsimile of its printed counterpart into a gateway to related knowledge, providing the research community with focused interactive access to analysis tools, external resources and the literature"

Optimized for life science-biomedical-biochemical scientific disciplines

Relies on external services; accessed via plug-ins whose appearance in the interface is mediated by a ‘semantic core’ for processing and analyzing data

Benefits to scholars and academic libraries

Academic libraries can offer enriched scientific articles by encouraging researchers to use Utopia Documents. The software is free and registration is only required when users want the comments function to be activated (to maintain the integrity of scientific discourse, anonymous comments are not allowed by Utopia). Some journals, such as the Biochemical Journal published by Portland Press, and journals published by the Royal Society of Chemistry, provide tags in their PDFs that enable Utopia Documents to extend its functionality. Thus you can render pictures of protein structures into dynamic, rotatable, 'manipulatable' 3D formats.

Data sources

The following data sources are accessed in Utopia Documents and activated automatically when there is relevant content to display:

Launched in 2011 by Labtiva with investments from Digital Science; ease of use and integrated search on PubMed and Google Scholar

daily recommendation service is based on your research interests and contents of your library; what does ReadCube add to reference management software? newly released PDF functionality? a bid by Labtiva to differentiate its product from competitors such as Mendeley, Zotero and EndNote Web

Utopia Documents and ReadCube both improve reading scholarly articles by combining static PDF content with data from the web; both apps fetch data from third-party databases and facilitate commenting/annotation of PDFs

Other reading apps

BrowZine, a virtual magazine stand, works by organizing articles found in open access and subscription databases, uniting them into complete journals, then arranging journals on an integrated newsstand; it is an easy and familiar way to read and monitor scholarly journals such as Elsevier, SAGE, Emerald, Wiley, and more. There are iPad, Android tablet and iPhone apps. You can save articles to your device to read offline.